Cotton root knot nematode (RKN) is a destructive nematode which forms galls on the roots of cotton plants. The causative agent is Meloidogyne incognita (Kofoid and White) Chitwood, a nematode which can infect a variety of plant species. Nutrient and water uptake are decreased in infected plants, and plants may become susceptible to other pathogens, especially Fusarium wilt (Minton, N. A. and Minton E. B., Phylopalhology 56:319-322 (1966)). Consequently, yield is decreased in plants infected with RKN. In the USA alone, an estimated 10.93% of cotton yield loss in 2004 was attributed to RKN (Blasingame and Patel, 2005). RKN is wide-spread throughout the US Cotton Belt. Methods to mitigate RKN damage include rotating cotton crops with non-susceptible crops and application of costly nematicides. However, the most effective way for cotton growers to reduce yield loss and crop damage due to RKN is to grow RKN resistant cotton cultivars. Therefore, a need exists for development of such RKN resistant cotton varieties and for methods to accelerate development of such varieties. Genetic markers can be used by plant breeders as an indirect means to select plants with favorable alleles. A major RKN resistance locus has been reported on Chromosome A11 (Kai, W. et al. Theor. Appl. Genet. 113:73-80 (2006)). Breeding for RKN resistant cotton varieties can be greatly facilitated by the use of marker-assisted selection for RKN resistance alleles. RKN resistance in cotton has been reported in different germplasm lines such as Auburn 623 RNR and Acala NemX. However, commercial cultivars with RKN resistance are limited. Identification of genetic markers associated with RKN resistance is of great value in a cotton breeding program. RAPD, AFLP, and RGA markers for identifying RKN resistant plants have been identified in a study using near-isogenic lines (NILs) (Niu, C. et al., Crop Science 47:9.51-960 (2007)). Genetic markers associated with RKN resistance in plants have also included SSR markers (Wang, C. et al. Theor. Appl. Genet. 112:770-777 (2006)).
Of the classes of markers, SNPs have characteristics which make them preferential to other genetic markers in detecting, selecting for, and introgressing RKN resistance in a cotton plant. SNPs are preferred because technologies are available for automated, high-throughput screening of SNP markers, which can decrease the time to select for and introgress RKN resistance in soybean plants. Further, SNP markers are ideal because the likelihood that a particular SNP allele is derived from independent origins in the extant population of a particular species is very low. As such, geneticly linked SNP markers are useful for tracking and assisting introgression of RKN resistance alleles, particularly in the case of RKN resistance haplotypes validated to exist in the resistant donor parent. A need exists for a SNP based marker set for identifying cotton plants resistant to RKN. The present invention provides a SNP based marker for identifying plants resistant to RKN.